- Get the Mind Badge and fight Team Aqua in the Seafloor Cavern. Then find the Sky Pillar (and Rayquaza and go back to the Sootopolis Gym and defeat Juan.
- Surf past the entrance to the Meteor Falls Cave, then travel up the large waterfall with HM07 Waterfall. Proceed through the cave until you encounter Bagon.
- Lower Bagon’s health with False Swipe and trap it with Sleep or Paralyze. Throw an Ultra Ball to get the best chance of capturing Bagon once and for all.
Getting HM07 Waterfall
Proceed through the story and get the Mind Badge. You'll need to complete most of the game's story before you can get Waterfall. This Hidden Move is required in order to access the area where you can find Bagon. Waterfall allows you to travel up waterfalls throughout the world. You'll get the Mind Badge in Mossdeep City.
Fight Team Aqua in the Seafloor Cavern. After getting the Mind Badge, you'll gain the ability to use Dive while traveling. Use this in the deep blue water south of Mossdeep to find the Seafloor Cavern.
Continue through Route 126 until you reach Sootopolis. If you've already been to Sootopolis, you can use Fly to reach it quickly. Find Steven on the north side of Sootopolis City.
Go to the Cave of Origin. You'll be asked by Steven to find Wallace in the Cave of Origin. Talk to Wallace and answer "SKY PILLAR".
Travel to the Sky Pillar and find Rayquaza at the top of the Pillar. You can get to the Sky Pillar from Pacifidlog Town. Rayquaza will fly off and head to Sootopolis City. Use Fly to follow.
Watch the scene and then head to the Sootopolis Gym. You'll find Rayquaza fighting of Groudon and Kyogre, and then it will fly off. Speak to Steven outside of the Sootopolis Gym, and then speak to Wallace. Wallace will give you HM07 as a thank you for saving the town.
Defeat Juan in the Sootopolis Gym. After getting Waterfall, you won't be able to use it outside of battle until you get the Rain Badge from the Sootopolis Gym. This is the final Gym in the game, so make sure that you're properly prepared for tough fights. Once you get the Rain Badge, you'll be able to use Waterfall around the world.
Finding Bagon
Head to the Meteor Falls Cave. You have already visited this cave earlier in the story, so Fly to Fallarbor Town to quickly reach Meteor Falls Cave. The cave is located between Route 114 and 115.
Surf on the water right past the entrance. After you enter Meteor Falls Cave, you'll come to a pool of water. Walk to the north and use Surf to travel across the water.
Use HM07 Waterfall to travel up the large waterfall. Approach the waterfall and press "A" to bring up the prompt to use Waterfall.
Enter the cave at the top of the waterfall. After climbing the waterfall, you'll see a small piece of land and a cave entrance. Get off on this small piece and walk through the entrance.
Walk to the north and climb down the ladder. Head to the right and then up a little bit to find a ladder. Take the ladder down to the lower level.
Walk around to the northwest corner of the cave and climb the ladder. You'll be challenged by a duo of trainers. After defeating them, use the stairs to climb to the top of the room.
Skip down the ledges, keeping to the left. The ladder you need to reach is in the bottom-left corner of the room. Skip down the ledges and stay left to reach the ladder.
Walk down the stairs and Surf on the water. Make your way to the north side of the room and get off on the piece of land with the cave entrance.
Enter the cave and Surf to the top of the room. This room is long and narrow, and you'll have to Surf across the water to cross the room. Get off on the small piece of land at the top of the room.
Walk around on the small piece of land until you encounter Bagon. This small patch of dry land is the only area in the entire game that you can encounter Bagon. Bagon has a 20% chance of appearing when you encounter a wild Pokémon here, so it may take several battles until one appears.
Catching Bagon
Use a Pokémon with False Swipe to lower Bagon's health. False Swipe is a great move for capturing Pokémon, as it can reduce the wild Pokémon's health down to 1 HP but will never knock it out. Farfetch'd, Cubone, Scizor, and Nincada are some of the Pokémon that can learn this move by leveling up, or you can use TM54 to teach it to a different Pokémon. If you don't have a Pokémon with False Swipe, you can use regular moves to lower Bagon's health as much as you can without knocking it out.
Use Sleep or Paralyze to trap the Bagon. These moves will increase the chances of your Poke Ball capturing Bagon. There are lots of Pokémon that can learn moves that cause these conditions, and chances are you already have at least one.
Throw an Ultra Ball for the best chances of capturing Bagon. Ultra Balls are expensive, but they can catch the Bagon much more reliably than other balls. If you've lowered Bagon's health to 1 HP and it is asleep or paralyzed, just about any Poke Ball should do the trick.
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